You can define your coordinates however is the most convenient for solving any particular problem. The simplest 2-d coordinate system for projectile motion problems would be to put the origin on the ground, with the x-axis horizontal and the y-axis vertical. That means y=0 is at ground level, so if you are 6 feet tall and throw a ball up, then y(t=0)=6', and Vy(0)= whatever velocity you release the ball at time t=0. The height at the top of the ball's travel will depend on Vy(0) at the release point y(0)=6' plus however long it takes for the ball to stop moving up. Use an equation like this...
y(t) = y(0) + Vy(0)*t + 1/2*ay*t^2
Where a = the acceleration due to gravity, which in this case is -9.8m/s^2.
Does that help?